Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate 206677 DVU1238 amino acid ABC transporter, periplasmic amino acid-binding protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >MicrobesOnline__882:206677 Length = 246 Score = 99.8 bits (247), Expect = 5e-26 Identities = 80/253 (31%), Positives = 125/253 (49%), Gaps = 13/253 (5%) Query: 1 MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60 M + VLL AL + + FA E+ + +A +PP + IVG D +A+ +E Sbjct: 1 MLQKVLLTVAALLLSTNVAFA-ERTVVFAHDATWPPMEFVDANKQIVGLAVDYVDAIAKE 59 Query: 61 MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGT 120 K V +DG+ L K DAI SS++IT++RKK++DFT Y++ LV+ T Sbjct: 60 AGFKVVHKNVAWDGIFAGLAAGKYDAIASSVTITEERKKAMDFTMPYFDVKQALVVPKTT 119 Query: 121 QVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVA 180 + + L ++KGK +G Q S FA + + G K Y D+ GR+DG V Sbjct: 120 E-AKTLEDMKGKTLGAQI-STTGHFA--IKRTAGVTAKSYDEIGLAMEDLFNGRIDGVVC 175 Query: 181 DATLLDDGFLKTD---SGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAI 237 D + + L+ + AF+ E Y GIAV++G+K +D IN I A+ Sbjct: 176 DDPVAANYALQQEEYAKKLKIAFIVDTPESEYY-----GIAVKQGNKELVDLINKGIEAV 230 Query: 238 RANGKYKQIQDKY 250 +A G Q++ K+ Sbjct: 231 KAKGIDAQLRAKW 243 Lambda K H 0.318 0.138 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 153 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 258 Length of database: 246 Length adjustment: 24 Effective length of query: 234 Effective length of database: 222 Effective search space: 51948 Effective search space used: 51948 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory